library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
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## filter, lag
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## intersect, setdiff, setequal, union
library(tidyr)
library(readr)
library(stringr)
library(ggplot2)
library(ggrepel)
library(topr)
library(UpSetR)
library(plyranges)
## Loading required package: BiocGenerics
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:dplyr':
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## combine, intersect, setdiff, union
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## IQR, mad, sd, var, xtabs
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## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
## table, tapply, union, unique, unsplit, which.max, which.min
## Loading required package: IRanges
## Warning: package 'IRanges' was built under R version 4.4.2
## Loading required package: S4Vectors
## Loading required package: stats4
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## Attaching package: 'S4Vectors'
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## Attaching package: 'IRanges'
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## collapse, desc, slice
## Loading required package: GenomicRanges
## Loading required package: GenomeInfoDb
## Warning: package 'GenomeInfoDb' was built under R version 4.4.2
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## Attaching package: 'plyranges'
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library(ieugwasr)
## OpenGWAS updates:
## Date: 2024-05-17
## [>] OpenGWAS is growing!
## [>] Please take 2 minutes to give us feedback -
## [>] It will help directly shape our emerging roadmap
## [>] https://forms.office.com/e/eSr7EFAfCG
library(gwascat)
## gwascat loaded. Use makeCurrentGwascat() to extract current image.
## from EBI. The data folder of this package has some legacy extracts.
# Source helper functions
source("multi_funcs.R")
Principal components
plot_ancestry_PCs("antidep-2501-mrmega-N06A.log")

plot_ancestry_PCs("antidep-2501-mrmega-N06AA.log")

plot_ancestry_PCs("antidep-2501-mrmega-N06AB.log")

Manhattan plots
mrmega_n06a <- get_sumstats("antidep-2501-mrmega-N06A-DIV.gz")
## Rows: 10650849 Columns: 29
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (5): MarkerName, EA, NEA, Effects, CHR
## dbl (23): Chromosome, Position, EAF, Nsample, Ncohort, beta_0, se_0, beta_1,...
## lgl (1): Comments
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
mrmega_n06aa <- get_sumstats("antidep-2501-mrmega-N06AA-DIV.gz")
## Rows: 9007284 Columns: 29
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (5): MarkerName, EA, NEA, Effects, CHR
## dbl (23): Chromosome, Position, EAF, Nsample, Ncohort, beta_0, se_0, beta_1,...
## lgl (1): Comments
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
mrmega_n06ab <- get_sumstats("antidep-2501-mrmega-N06AB-DIV.gz")
## Rows: 10033491 Columns: 29
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (5): MarkerName, EA, NEA, Effects, CHR
## dbl (23): Chromosome, Position, EAF, Nsample, Ncohort, beta_0, se_0, beta_1,...
## lgl (1): Comments
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
mrmega_n06a_assoc <- get_assoc(mrmega_n06a, "N06A")
mrmega_n06aa_assoc <- get_assoc(mrmega_n06aa, "N06AA")
mrmega_n06ab_assoc <- get_assoc(mrmega_n06ab, "N06AB")
plot_manhat(mrmega_n06a_assoc)

plot_manhat(mrmega_n06aa_assoc)

plot_manhat(mrmega_n06ab_assoc)

Clumps
clumps_N06A <- get_clumps("antidep-2501-mrmega-N06A-DIV.clumps.tsv")
## Rows: 26 Columns: 32
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (5): MarkerName, EA, NEA, Effects, CHR
## dbl (26): Locus, Chromosome, Position, EAF, Nsample, Ncohort, beta_0, se_0, ...
## lgl (1): Comments
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
clumps_N06AA <- get_clumps("antidep-2501-mrmega-N06AA-DIV.clumps.tsv")
## Rows: 2 Columns: 32
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (4): MarkerName, EA, NEA, Effects
## dbl (27): Locus, Chromosome, Position, EAF, Nsample, Ncohort, beta_0, se_0, ...
## lgl (1): Comments
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
clumps_N06AB <- get_clumps("antidep-2501-mrmega-N06AB-DIV.clumps.tsv")
## Rows: 6 Columns: 32
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (5): MarkerName, EA, NEA, Effects, CHR
## dbl (26): Locus, Chromosome, Position, EAF, Nsample, Ncohort, beta_0, se_0, ...
## lgl (1): Comments
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
clumps_N06A
clumps_N06AA
clumps_N06AB
Catalogue
gwcat <- get_cached_gwascat()
gwascat_N06A_table <- look_up_snps(clumps_N06A, gwcat)
gwascat_N06AA_table <- look_up_snps(clumps_N06AA, gwcat)
gwascat_N06AB_table <- look_up_snps(clumps_N06AB, gwcat)
write.csv(gwascat_N06A_table, "multi_files/gwas_cat_N06A_table.csv", quote = F, row.names = F)
write.csv(gwascat_N06AA_table, "multi_files/gwas_cat_N06AA_table.csv", quote = F, row.names = F)
write.csv(gwascat_N06AB_table, "multi_files/gwas_cat_N06AB_table.csv", quote = F, row.names = F)